The Toba supereruption (Youngest Toba Tuff or simply YTT[1]) was a supervolcaniceruption that is believed to have occurred sometime between 69,000 and 77,000 years ago at Lake Toba (Sumatra, Indonesia). It is recognized as one of the Earth‘s largest known eruptions. The related catastrophe hypothesis holds that this event plunged the planet into a 6-to-10-year volcanic winter and possibly an additional 1,000-year cooling episode. This change in temperature is hypothesized to have resulted in the world’s human population being reduced to 10,000 or even a mere 1,000 breeding pairs, creating a bottleneck in human evolution.

Supereruption

The Toba eruption or Toba event[2] occurred at what is now Lake Toba about 73,000±4,000 years[3][4] ago. The Toba eruption was the latest of the three major eruptions which occurred at Toba in the last 1 million years.[5] The last eruption had an estimated Volcanic Explosivity Index of 8 (described as “mega-colossal”), or magnitude ≥ M8; it thus made a sizeable contribution to the 100 × 30 km2caldera complex.[6]Dense-rock equivalent estimates of eruptive volume for the eruption vary between 2,000 km3 and 3,000 km3, but the most frequently quoted DRE is 2,800 km3 (about 7×1015 kg) of erupted magma, of which 800 km3 was deposited as ash fall.[7] It was two orders of magnitude greater in erupted mass than the largest volcanic eruption in historic times, in 1815 at Mount Tambora in Indonesia, which caused the 1816 “Year Without a Summer” in the northern hemisphere.[8]

Although the Toba eruption took place in Indonesia, it deposited an ash layer approximately 15 centimetres thick over the entirety of South Asia. A blanket of volcanic ash was also deposited over the Indian Ocean, and the Arabian and South China Sea.[9] Deep-sea cores retrieved from the South China Sea extended the known distribution of the eruption and suggest that the 2,800 km3 calculation of the eruption magnitude is a minimum value or even an underestimate.[10]

Volcanic winter and cooling

The apparent coincidence of the eruption with the onset of the last glacial period attracted the scientists’ interest. Michael L. Rampino and Stephen Self argued that the eruption caused a “brief, dramatic cooling or ‘volcanic winter'”, which resulted in a global mean surface temperature drop of 3–5 °C and accelerated the glacial transition from warm to cold temperatures of the last glacial cycle.[11] Zielinski showed Greenlandice core evidence for a 1,000-year cool period with low δ18O and increased dust deposition immediately following the eruption. He further suggested that this 1,000-year cool period (stadial) could have been caused by the eruption, and that the longevity of the Toba stratospheric loading may account at least for the first two centuries of the cooling episode.[12] Rampino and Self believe that global cooling was already underway at the time of the eruption, but the procedure was extremely slow; YTT “may have provided the extra ‘kick’ that caused the climate system to switch from warm to cold states.”[13] Oppenheimer discounts the arguments that the eruption triggered the last glaciation,[14] but he accepts that it may have been responsible for a millennium of cool climate prior to the Dansgaard-Oeschger event.[15]

According to Alan Robock,[16] the Toba incident did not initiate an ice age. Using an emission of 6 billion tons of sulphur dioxide, his simulations demonstrated a maximum global cooling of around 15 °C, approximately three years after the eruption. As the saturated adiabatic lapse rate is 4.9 °C/1,000 m for temperatures above freezing,[17] this means that the tree line and the snow line were around 3,000 m (9,900 ft) lower at this time. Nevertheless, the climate recovered over a few decades. Robock found no evidence that the 1,000-year cold period seen in Greenland ice core records was directly generated by the Toba eruption. Nevertheless, he argues that the volcanic winter would have been colder and longer-lasting than Ambrose assumed, which strengthens his argument for a genetic bottleneck. Contrary to Robock, Oppenheimer believes that estimates of a surface temperature drop of 3–5 °C after the eruption are probably too high; a figure closer to 1 °C appears more realistic.[18] Robock criticized Oppenheimer’s analysis, arguing that it is based on simplistic T-forcing relationships.[19]

Despite the different approaches and estimates, scientists agree that a supereruption like the one at Lake Toba must have led to very extensive ash-fall layers and injection of noxious gases into the atmosphere, having severe worldwide effects on climate and weather.[20] Additionally, the Greenland ice core data display an abrupt climate change around this time,[21] but there is no consensus that the eruption directly generated the 1,000-year cold period seen in Greenland or triggered the last glaciation.[22]

Genetic bottleneck theory

Ann Gibbons first suggested, in an article in the October 1993 edition of Science, that a bottleneck in human evolution about 50,000 years ago could be linked to the Toba eruption.[23] Rampino and Self backed up this idea in a letter to the journal later that year.[24] The bottleneck theory was then further developed by Ambrose in 1998 and Rampino & Ambrose in 2000, who invoked the Toba eruption to explain a severe culling of the human population.[25]

According to the supporters of the genetic bottleneck theory, between 50,000 and 100,000 years ago, human population suffered a severe population decrease—only 3,000 to 10,000 individuals survived—followed eventually by rapid population increase, innovation, progress and migration.[26] Several geneticists, including Lynn Jorde and Henry Harpending, have proposed that the human race was reduced to approximately five to ten thousand people.[27] Genetic evidence suggests that all humans alive today, despite apparent variety, are descended from a very small population, perhaps between 1,000 to 10,000 breeding pairs about 70,000 years ago.[28] Note that this is an estimate of ancestors, not of total human population. Isolated human populations that eventually died out without descendants may have also existed in numbers that cannot be estimated by geneticists.

Ambrose and Rampino proposed in the late 1990s that a genetic bottleneck could have been caused by the climate effects of the Toba eruption. The supporters of the Toba catastrophe theory suggest that the eruption resulted in a global ecological disaster with extreme phenomena, such as worldwide vegetation destruction, and severe drought in the tropical rainforest belt and in monsoonal regions. Τhis massive environmental change created population bottlenecks in species that existed at the time, including hominids;[29] this in turn accelerated differentiation of the reduced human population. Therefore, Toba may have caused modern races to differentiate abruptly only 70,000 years ago, rather than gradually over one million years.[30] Robock believes that, indeed, a 10-year volcanic winter triggered by YTT could have largely destroyed the food supplies of humans and therefore caused a significant reduction in population sizes.[31]

Gene analysis of some genes shows divergence anywhere from 60,000 to 2 million years ago. This does not contradict the Toba theory, however, because Toba is not conjectured to be an extreme bottleneck event. The complete picture of gene lineages, including present-day levels of human genetic variation, allows the theory of a Toba-induced human population bottleneck.[32]

However, research by archaeologist Michael Petraglia’s team cast doubt on Ambrose’s theory. Petraglia and his team found stone tools in southern India, above and below a thick layer of ash from the Toba eruption. The tools from each layer were remarkably similar, and Petraglia says that this shows that the huge dust clouds from the eruption did not wipe out the local population of people:[33][34][35][36][37]

A 2009 study by Martin A. J. Williams’s team challenges Petraglia’s findings. Williams analysed pollen from a marine core in the Bay of Bengal with stratified Toba ash, and argued that the eruption caused prolonged deforestation in South Asia. Ambrose, who is a co-author of the study, calls the evidence “unambiguous”, and further argues that YTT may have forced our ancestors to adopt new survival strategies, which permitted them to replace Neanderthals and “other archaic human species”.[38] However, both Neanderthals in Europe and the small-brained Homo floresiensis in Southeastern Asia survived YTT by 50,000 and 60,000 years respectively.[39]

Oppenheimer accepts that the arguments proposed by Rampino and Ambrose are plausible, but they are not yet compelling for two reasons: it is difficult to estimate the global and regional climatic impacts of the eruption, and, at the same time, we cannot conclude with any confidence that the eruption actually preceded the bottleneck.[40] Furthermore, a 2010 geneticists’ study seems to question the foundations of the Toba bottleneck theory: analysis of Alu sequences across the entire human genome has shown that the effective human population was already less than 26,000 as far back as 1.2 million years ago, suggesting that no Toba bottleneck was necessary. Possible explanations for the low population size of human ancestors may include repeated population bottlenecks or periodic replacement events from competing Homo subspecies.[41]

This is consistent with the Toba catastrophe theory which suggests that a bottleneck of the human population occurred c. 70,000 years ago, proposing that the human population was reduced to c. 15,000 individuals[43] when the Tobasupervolcano in Indonesia erupted and triggered a major environmental change, including a volcanic winter. The theory is based on geological evidences of sudden climate change at that time, and on coalescence evidences of some genes (including mitochondrial DNA, Y-chromosome and some nuclear genes)[44] and the relatively low level of genetic variation among present-day humans.[43]

However, such coalescence is genetically expected and does not, in itself, indicate a population bottleneck, because mitochondrial DNA and Y-chromosome DNA are only a small part of the entire genome, and are atypical in that they are inherited exclusively through the mother or through the father, respectively. Most genes in the genome are inherited randomly from either father or mother, thus can be traced back in time via either matrilineal or patrilineal ancestry.[45] Research on many (but not necessarily most) genes find various coalescence points from 2 million years ago to 60,000 years ago, according to the genes considered, thus disproving the existence of more recent extreme bottlenecks (i.e. a single breeding pair).[43][46]

On the other hand, in 2000, a Molecular Biology and Evolution paper suggested a transplanting model or a ‘long bottleneck’ to account for the limited genetic variation, rather than a catastrophic environmental change.[47] This would be consistent with suggestions that in sub-Saharan Africa human populations could have dropped at times as low as 2,000, for perhaps as long as 100,000 years, before numbers began to expand again in the Late Stone Age[48]

TMRCAs of loci, Y chromosome, and mitogenomes compared to their probability distributions if one assumes that population expanded 75kya from a long-standing population of 11,000 effective individuals

One early oversight of many early studies is that the fixation of alleles (the object of coalescent theory study) is not a discrete mathematical function, but a probabilistic function, and it is highly dependent on the ploidy being studied.

Takahata (1999) was the first molecular anthropologist to point out that conclusions drawn from single locus studies suffer from the large randomness of the fixation process. Schaffner (2004) has cleared up this issue by demonstrating the three sets of fixation ranges, haploid, X-linked and diploid where TMRCAs for different loci are expected to fall. Takahata (1993) estimated the effective human population size at 11,000 individuals, and Schaffner working on an improved set of X-linked markers from low recombination regions of the X-chromosome identified an effective size of approximately 12,000 individuals.[49][50] PDHA1 falls on the edge of fixation times for X-linked chromosome. For autosomes, the MX1 locus and the HLA loci appear to preserve past diversity in the human population. With few exceptions, however, X-linked and autosomes appear to coalesce under a common population size.

Just as mitochondria are inherited matrilineally, Y-chromosomes are inherited patrilineally.[51] Y chromosomal TMRCA, the time of the Y-chromosomal Adam, lie in the 42 to 110ky range, which is a little less than half the TMRCA of mtDNA. Importantly, the genetic evidence suggests that the most recent patriarch of all humanity is much more recent than the most recent matriarch, suggesting that ‘Adam’ and ‘Eve’ were not alive at the same time. While ‘Eve’ is believed to have lived more than 140,000 years ago, ‘Adam’ appears to have lived less than 110,000 years ago.[43] According to Wilder et al. (2004), the lower TMRCA of Y is due to an effective population size of males 1/2 that of females over most of human evolution.[52]

Even with a reduced effective population size there are problems with this explanation. Recently, with more mitogenomic sequences from Africa, evidence has grown for an early population size expansion. This expansion probably started prior to 100,000 years ago and greatly increasing after 100,000 years ago. The effective size of the human population should have well exceeded 104 individuals between 80,000 to 120,000 years ago. Given this expansion, implicit male populations sizes would have improbably coalesced to Y-Adam within that time frame. However, the greatest age for Y TMRCA is more recent than the evidence for expansion. In addition, despite evidence of a bottleneck, the human mtDNA TMRCA range remains consistent with population sizes estimates from X-linked and autosomal loci. However, Y-chromosomes TMRCA is not consistent with mtDNA or either of these sets (see figure:TMRCAs of loci).

This inconsistency may be explained by some form of Y chromosome selection (cultural, or genetic). A Y-chromosomal lineage might have swept the male population.[53] However, if true the place of greatest Y chromosomal diversity could be anywhere that humans inhabited Africa. However, Y diversity is greatest in Southern Africa, close to the earliest female population split predicted by Behar et al. (2009) suggesting the earliest branch in Y should be between 125,000 and 150,000 Ka in age. This suggests a SNP rate inaccuracy in the Y-chromosomal and/or mtDNA molecular clock. A recent study of X-chromosome suggests that different rates of male sperm production between humans and chimps has altered the molecular clock in sex chromosomes.[54] This shift in the molecular clock would not affect the mtDNA SNP rate and would affect the Y-chromosomal rate more than X-linked and autosomes, since these Y-chromosomal lineages spend the most time in male testes.

The term bottleneck has been used to describe the population structure that created mtDNA Eve. The appearance of a bottleneck was a consequence of the appearance of a ‘big bang’ of HVR branching about the time humans first left Africa. From that point back to the TMRCA was less than 100,000 years and the population size estimate was below 5000 effective females. Looking backwards in time this is what might be called a retrograde bottleneck, however it is an artifact of coalescence process, since the coalescence of mitogenomes on the sequence of the MRCA (the event which initiated with mtDNA Eve and extended to the extant population) conceals the population size from all points earlier than that mutation (see figure Retrograde look at bottlenecks). Therefore the population size could have been of equal size going back 100,000s of years, to the time in which Neanderthals’ ancestors and Modern humans’ ancestors were part of a single population.

Evidence against a population bottleneck

The work done on Neanderthal sequencing (Green 2007) has identified little evidence of Neanderthal contribution to humans, moreover it describes an effective size of the population when humans and Neanderthals split was about 3000 individuals. Taken in the light of Schaffner’s and Takahata’s effective populations sizes, 3000 < Ne, female < 6000 and 2000 < Ne, male < 4000 does not appear to represent a magnitude shift downward from the average size. Taking a null hypothesis, prior to and after the mtDNA MRCA population sizes appear to reflect long-term small population structure up until 70,000~150,000 years ago, not a brief constricting bottleneck, but a long period of constrained size followed by an expansion.

Evidence for a population bottleneck

Confidence intervals of population size do not require an alternative, population bottleneck, hypothesis. However, a bottleneck may have existed. If the population size were at 12,000 individuals as suggested by X-chromosomal studies, the Ne for mtDNA and Y in particular, is below the expected median TMRCAs (See image Above and on the left). Y chromosome and mtDNA may be more representative of population structure immediately prior to expansion. However, meshing mtDNA TMRCA and Y TMRCA is problematic. If these two loci could be treated together, they would likely fall significantly below the X-linked and autosome-derived size estimates for any given TCHLCA.

Most probable number of effective females based on TMRCA, showing the best estimate, and how Takahata’s and Shaffners estimates compare (after conversion of Ne to Ne females)

Atkinson, Gray & Drummond (2009) show that prior to 150,000 years ago the population could have been as low as 1000 effective females (~1500 total, 4500 census) and as high as 11,000 effective females with a lower population size between 150,000 to 200,000 years ago. Whereas X-chromosome and autosomes warrant larger population size minima, thousands of females, these loci of larger ploidy are capable of sensing population structure of much longer periods. Such periods may include recent and ancient population structures and size oscillations. Most population structure models for Africa have assumed much of the growth occurred very recently, however Atkinson et al. (2009) shows that by 100,000 years ago the minimum female population size exceed the estimated population size for females. The flat population/recent growth model is troubled in considering an ancient population core in Tanzania (Gonder. et al. (2007) early East African/Khoisan split (Behar et al. 2008), and spread of L2 in parts of Africa where L0 and L1 are found in low abundance. Simply, the evidence of lineage growth appears to correlate with growth in geographic regions in which humans live. Retrospectively, this suggests that population size was growing as new lineages appears to expand territory. Comparing these observations with populations sizes suggested by X-chromosome (~7000 females) one might expect a low stand of the human population size of 1/3 to 1/2 this size between 150,000 to 250,000 years ago. This indicates that earlier periods had a reciprocal, or larger size (>7000 females) between 200,000 and 500,000 years ago.

Other authors such as Endicott et al. (2009) think that bottlenecks in the human prehistory were such a common feature that they interfere with TMRCA determinations and imply the possible effect of the OIS-6 on population size reduction with a TMRCA around the time of late pliestocene climate optimum, approximately 120,000 years ago.

Human parasite: analysis of louse genes

Alan Rogers, a co-author of this study and professor of anthropology at the University of Utah, says: “The record of our past is written in our parasites.” Rogers and others have proposed the bottleneck may have occurred because of a mass die-off of early humans due to a globally catastrophic volcanic eruption. The analysis of louse genes confirmed that the population of Homo sapiens mushroomed after a small band of early humans left Africa sometime between 150,000 and 50,000 years ago.[55]

Human pathogen: analysis of Helicobacter pylori genes

Recent research states that genetic diversity in the pathogenic bacteriumHelicobacter pylori decreases with geographic distance from East Africa, the birthplace of modern humans. Using the genetic diversity data, the researchers have created simulations that indicate the bacteria seem to have spread from East Africa around 58,000 years ago. Their results indicate modern humans were already infected by H. pylori before their migrations out of Africa, and H. pylori remained associated with human hosts since that time.[56]

Genetic bottlenecks of other mammals

The eruption may have also caused bottlenecks or extinctions in some animals (especially those in Southeast Asia, India, far north as China and as far west as Europe and Africa). The populations of the Eastern African chimpanzee,[57] Bornean orangutan,[58] central Indian macaque,[59] the cheetah, the tiger,[60] and the separation of the nuclear gene pools of eastern and western lowland gorillas,[61] all recovered from very low numbers around 70,000–55,000 years ago.

Migration after Toba

It is currently not known where human populations were living at the time of the eruption. The most plausible scenario is that all the survivors were populations living in Africa, whose descendants would go on to populate the world. However, recent archeological finds, mentioned above, have suggested that a human population may have survived in Jwalapuram, Southern India.[62]

Recent analyses of mitochondrial DNA have set the estimate for the major migration from Africa from 60,000–70,000 years ago,[63] around 10–20,000 years earlier than previously thought, and in line with dating of the Toba eruption to around 66,000–76,000 years ago. During the subsequent tens of thousands of years, the descendants of these migrants populated Australia, East Asia, Europe, and the Americas.